# Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics Identifications

## Documentation for package ‘MSnID’ version 1.40.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Code demos. Use demo() to run them.
- Package NEWS.

## Help Pages

MSnID-package | MSnID: Utilities for Handling MS/MS Identifications
$-method | The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data
$-method | The "MSnIDFilter" Class for Handling MS/MS Criteria, Relationships and Thresholds for Data Filtration.
$<--method | The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data
$<--method | The "MSnIDFilter" Class for Handling MS/MS Criteria, Relationships and Thresholds for Data Filtration.
accessions | Non-redundant list of accession (protein) identifiers
accessions-method | The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data
add_mod_symbol | Annotates peptide sequences with modification symbols
add_mod_symbol-method | Annotates peptide sequences with modification symbols
apply_filter | Filters the MS/MS identifications
apply_filter-method | Filters the MS/MS identifications
as.numeric-method | The "MSnIDFilter" Class for Handling MS/MS Criteria, Relationships and Thresholds for Data Filtration.
assess_missed_cleavages | Counts the missing cleavage sites within the peptides sequence
assess_missed_cleavages-method | The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data
assess_termini | Checks if the peptide termini conforms with cleavage specificity
assess_termini-method | The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data
class:MSnID | The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data
class:MSnIDFilter | The "MSnIDFilter" Class for Handling MS/MS Criteria, Relationships and Thresholds for Data Filtration.
coerce-method | The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data
correct_peak_selection | Corrects wrong selection of monoisotopic peak
correct_peak_selection-method | The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data
c_elegans | Example mzIdenML File and MSnID Object
dim-method | The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data
evaluate_filter | Filters the MS/MS identifications
evaluate_filter-method | The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data
fetch_conversion_table | Fetches conversion table form one type of identifiers to another
id_quality | Identification quality
id_quality-method | The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data
infer_parsimonious_accessions | Eliminates Redundancy in Peptide-to-Protein Mapping
infer_parsimonious_accessions-method | Eliminates Redundancy in Peptide-to-Protein Mapping
length-method | The "MSnIDFilter" Class for Handling MS/MS Criteria, Relationships and Thresholds for Data Filtration.
map_mod_sites | Maps the modifications to protein sequence
map_mod_sites-method | Maps the modifications to protein sequence
mass_measurement_error | Computes error of the parent ion mass to charge measurement
mass_measurement_error-method | The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data
MSnID | The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data
MSnID-class | The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data
MSnIDFilter | The "MSnIDFilter" Class for Handling MS/MS Criteria, Relationships and Thresholds for Data Filtration.
MSnIDFilter-class | The "MSnIDFilter" Class for Handling MS/MS Criteria, Relationships and Thresholds for Data Filtration.
msnidObj | Example mzIdenML File and MSnID Object
names-method | The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data
names-method | The "MSnIDFilter" Class for Handling MS/MS Criteria, Relationships and Thresholds for Data Filtration.
optimize_filter | Filter criteria optimization to maximize the number of identifications given the FDR upper threshold
optimize_filter-method | Filter criteria optimization to maximize the number of identifications given the FDR upper threshold
peptides | Non-redundant list of peptides
peptides-method | The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data
proteins | Non-redundant list of accession (protein) identifiers
proteins-method | The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data
psms | Peptide-to-spectrum matches
psms-method | The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data
psms<- | Peptide-to-spectrum matches
psms<--method | The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data
read_mzIDs | Populates MS/MS results table from mzIdentML files
read_mzIDs-method | The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data
recalibrate | Post-experimental recalibration of observed mass to charge ratios
recalibrate-method | The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data
remap_accessions | Changes accessions from one protein id to another
remap_accessions-method | Changes accessions from one protein id to another
remap_fasta_entry_names | Remapping entries in FASTA file
report_mods | Lists modification masses in the MSnID object
report_mods-method | Lists modification masses in the MSnID object
show-method | The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data
show-method | The "MSnIDFilter" Class for Handling MS/MS Criteria, Relationships and Thresholds for Data Filtration.
update-method | The "MSnIDFilter" Class for Handling MS/MS Criteria, Relationships and Thresholds for Data Filtration.
[[-method | The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data
[[<--method | The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data